 Bar Ilan University Faculty of Medicine |
Perl Programming for Bioinformatics and the Internet
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Description
This course provides an introduction to Perl Programming for Bioinformatics and the Internet. The course starts off from the basics and no prior programming skills are required. The course covers scalar data, array functions, control structures, file I/O (input/output), hashess, sorting, loop control, regular expressions, and CGI programming for the internet. The class meetings comprise frontal lectures, and the coursework includes writing functionl programs. The course is open to graduate students from all faculties.
The course meets on Thursdays at 10:30-11:30 in room 102 of the Faculty of Medicine. The exercise session takes place in the computer class, room 211, at 11:30-13:00.
Schedule
| Date | Topic | Book | Assignment | Help files |
| Thursday 30/10 | Introduction | Backround | Basic Linux commands | |
| Thursday 6/11 | Scalar data & Operators | Ch. 1-2 | Assignment 1, Assignment 2 | |
| Thursday 13/11 | Arrays | Ch. 1-2 | ||
| Thursday 20/11 | Control structures, Functions | Ch. 3-4, 7 | Assignment 3 | |
| Thursday 27/11 | File I/O, basic text processing | Ch. 3-4 | Assignment 4 | |
| Thursday 4/12 | Hashes, Loop controls, Sorting | Ch. 3-4 | Assignment 5 | |
| Thursday 11/12 | Perl modules | Ch. 4 | ||
| Thursday 18/12 | Regular Expressions | Ch. 5 | Assignment 6 | |
| Thursday 25/4 | No Class (Chanuka vacation) | |||
| Thursday 1/1 | No Class (Asara Betevet) | |||
| Thursday 8/1 | CGI programming | Ch. 19 | Assignment 7,Assignment 8 | |
| Thursday 15/1 | Graphical representation of data | |||
| Thursday 22/1 | References and data structures | |||
| Thursday 29/1 | Process management | Final assignment |
Related Courses
- Jaime Prilusky
Feinberg Graduate School
Weizmann Institute of Science
"Perl for Bioinformatics"
Coursework
- Bibliography
- Programming Perl, 3rd edition, by Larry Wall, O'Reilly.
- Beginning Perl for Bioinformatics, by James Tisdall, O'Reilly Media
- Class Participation
- Attend for your own benefit.
- Contribute ideas during all class discussions
- Course Projects
- At the end of each class there will be a home exercise to be submitted by the beginning of next class. At the end of the course, there will be a final project.
- The combined excercises are worth 60 points in the final grade, and the final project is worth 40 points in the final grade.
- The final project of last year resulted in the following publication:
Students
- Faculty of Medicine
- Or Ehrlich
- Ilya Mistesky
- Michael Rosen
- Yoav Bahat
- Fadwa Dabach
- Efrat Shuster
- Sivan Eliahu
- Etadel Morad
- Shelly Yossifovich
- Noa Landau
- Michael Gvurian
- Ron Eitan
- Roey Reisfeld
- Nir Werbner